Hello
I'm new to Ray, and was hoping someone can help me with this error. We can get
Ray to produce contigs and scaffolds and that worked fine. Then we installed
the optional stuff for Ray Communities to work, but it is giving us an error...
This was Ray 2.2.0 running on four nodes using OpenMPI 1.6.5 on Centos 6.x
We are currently running a small file with a few thousand reads to test, does
that matter?
Here is the last part of the output:
...
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2384 objects=2
globalHandle=2384
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2400 objects=1
globalHandle=2400
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2416 objects=1
globalHandle=2416
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2432 objects=1
globalHandle=2432
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2448 objects=2
globalHandle=2448
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2464 objects=1
globalHandle=2464
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2480 objects=1
globalHandle=2480
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2496 objects=1
globalHandle=2496
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2512 objects=1
globalHandle=2512
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2528 objects=2
globalHandle=2528
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2544 objects=1
globalHandle=2544
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2560 objects=3
globalHandle=2560
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2576 objects=1
globalHandle=2576
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2592 objects=2
globalHandle=2592
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2608 objects=1
globalHandle=2608
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2624 objects=1
globalHandle=2624
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2640 objects=1
globalHandle=2640
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 Sending RAY_MPI_TAG_SEARCH_ELEMENTS directory=0 file=2656 objects=1
globalHandle=2656
Received RAY_MPI_TAG_SEARCH_ELEMENTS from 0
Sending a reply with RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY to 0
received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work
Rank 0 synced
scripts/NCBI-Taxonomy/NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes/
Synchronized counts.
[node003:65346] *** Process received signal ***
[node003:65346] Signal: Segmentation fault (11)
[node003:65346] Signal code: Address not mapped (1)
[node003:65346] Failing at address: (nil)
[Braves004:62891] *** Process received signal ***
[Braves004:62891] Signal: Segmentation fault (11)
[Braves004:62891] Signal code: Address not mapped (1)
[Braves004:62891] Failing at address: (nil)
[Braves002:40003] *** Process received signal ***
[Braves002:40003] Signal: Segmentation fault (11)
[Braves002:40003] Signal code: Address not mapped (1)
[Braves002:40003] Failing at address: (nil)
[node003:65347] *** Process received signal ***
[node003:65347] Signal: Segmentation fault (11)
[node003:65347] Signal code: Address not mapped (1)
[node003:65347] Failing at address: (nil)
[Braves004:62892] *** Process received signal ***
[Braves004:62892] Signal: Segmentation fault (11)
[Braves004:62892] Signal code: Address not mapped (1)
[Braves004:62892] Failing at address: (nil)
[node003:65348] *** Process received signal ***
[node003:65348] Signal: Segmentation fault (11)
[node003:65348] Signal code: Address not mapped (1)
[node003:65348] Failing at address: (nil)
[Braves004:62893] *** Process received signal ***
[Braves004:62893] Signal: Segmentation fault (11)
[Braves004:62893] Signal code: Address not mapped (1)
[Braves004:62893] Failing at address: (nil)
[Braves002:40004] *** Process received signal ***
[Braves002:40004] Signal: Segmentation fault (11)
[Braves002:40004] Signal code: Address not mapped (1)
[Braves002:40004] Failing at address: (nil)
[node003:65349] *** Process received signal ***
[node003:65349] Signal: Segmentation fault (11)
[node003:65349] Signal code: Address not mapped (1)
[node003:65349] Failing at address: (nil)
[Braves004:62894] *** Process received signal ***
[Braves004:62894] Signal: Segmentation fault (11)
[Braves004:62894] Signal code: Address not mapped (1)
[Braves004:62894] Failing at address: (nil)
[Braves002:40005] *** Process received signal ***
[Braves002:40005] Signal: Segmentation fault (11)
[Braves002:40005] Signal code: Address not mapped (1)
[Braves002:40005] Failing at address: (nil)
[Braves002:40006] *** Process received signal ***
[Braves002:40006] Signal: Segmentation fault (11)
[Braves002:40006] Signal code: Address not mapped (1)
[Braves002:40006] Failing at address: (nil)
[node003:65346] [ 0] /lib64/libpthread.so.0() [0x32b2c0f520]
[node003:65346] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x5092fa]
[node003:65346] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500471]
[node003:65346] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f626]
[node003:65346] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576258]
[node003:65346] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdc1]
[node003:65346] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4c0]
[node003:65346] [ 7] Ray(main+0xc5) [0x46d145]
[node003:65346] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x32b281ec9d]
[node003:65346] [ 9] Ray() [0x4691a9]
[node003:65346] *** End of error message ***
[Braves004:62894] [ 0] /lib64/libpthread.so.0() [0x3a53c0f520]
[Braves004:62894] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves004:62894] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves004:62894] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves004:62894] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves004:62894] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves004:62894] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves004:62894] [ 7] Ray(main+0xc5) [0x46d155]
[Braves004:62894] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3a5381ec9d]
[Braves004:62894] [ 9] Ray() [0x4691b9]
[Braves004:62894] *** End of error message ***
[node003:65347] [ 0] /lib64/libpthread.so.0() [0x32b2c0f520]
[node003:65347] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x5092fa]
[node003:65347] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500471]
[node003:65347] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f626]
[node003:65347] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576258]
[node003:65347] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdc1]
[node003:65347] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4c0]
[node003:65347] [ 7] Ray(main+0xc5) [0x46d145]
[node003:65347] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x32b281ec9d]
[node003:65347] [ 9] Ray() [0x4691a9]
[node003:65347] *** End of error message ***
[Braves004:62891] [ 0] /lib64/libpthread.so.0() [0x3a53c0f520]
[Braves004:62891] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves004:62891] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves004:62891] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves004:62891] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves004:62891] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves004:62891] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves004:62891] [ 7] Ray(main+0xc5) [0x46d155]
[Braves004:62891] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3a5381ec9d]
[Braves004:62891] [ 9] Ray() [0x4691b9]
[Braves004:62891] *** End of error message ***
[Braves002:40006] [ 0] /lib64/libpthread.so.0() [0x3dc140f520]
[Braves002:40006] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves002:40006] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves002:40006] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves002:40006] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves002:40006] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves002:40006] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves002:40006] [ 7] Ray(main+0xc5) [0x46d155]
[Braves002:40006] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3dc101ec9d]
[Braves002:40006] [ 9] Ray() [0x4691b9]
[Braves002:40006] *** End of error message ***
[Braves004:62892] [ 0] /lib64/libpthread.so.0() [0x3a53c0f520]
[Braves004:62892] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves004:62892] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves004:62892] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves004:62892] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves004:62892] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves004:62892] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves004:62892] [ 7] Ray(main+0xc5) [0x46d155]
[Braves004:62892] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3a5381ec9d]
[Braves004:62892] [ 9] Ray() [0x4691b9]
[Braves004:62892] *** End of error message ***
[Braves002:40003] [ 0] /lib64/libpthread.so.0() [0x3dc140f520]
[Braves002:40003] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves002:40003] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves002:40003] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves002:40003] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves002:40003] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves002:40003] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves002:40003] [ 7] Ray(main+0xc5) [0x46d155]
[Braves002:40003] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3dc101ec9d]
[Braves002:40003] [ 9] Ray() [0x4691b9]
[Braves002:40003] *** End of error message ***
[node003:65348] [ 0] /lib64/libpthread.so.0() [0x32b2c0f520]
[node003:65348] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x5092fa]
[node003:65348] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500471]
[node003:65348] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f626]
[node003:65348] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576258]
[node003:65348] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdc1]
[node003:65348] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4c0]
[node003:65348] [ 7] Ray(main+0xc5) [0x46d145]
[node003:65348] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x32b281ec9d]
[node003:65348] [ 9] Ray() [0x4691a9]
[node003:65348] *** End of error message ***
[node003:65349] [ 0] /lib64/libpthread.so.0() [0x32b2c0f520]
[node003:65349] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x5092fa]
[node003:65349] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500471]
[node003:65349] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f626]
[node003:65349] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576258]
[node003:65349] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdc1]
[node003:65349] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4c0]
[node003:65349] [ 7] Ray(main+0xc5) [0x46d145]
[node003:65349] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x32b281ec9d]
[node003:65349] [ 9] Ray() [0x4691a9]
[node003:65349] *** End of error message ***
[Braves004:62893] [ 0] /lib64/libpthread.so.0() [0x3a53c0f520]
[Braves004:62893] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves004:62893] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves004:62893] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves004:62893] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves004:62893] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves004:62893] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves004:62893] [ 7] Ray(main+0xc5) [0x46d155]
[Braves004:62893] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3a5381ec9d]
[Braves004:62893] [ 9] Ray() [0x4691b9]
[Braves004:62893] *** End of error message ***
[Braves002:40004] [ 0] /lib64/libpthread.so.0() [0x3dc140f520]
[Braves002:40004] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves002:40004] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves002:40004] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves002:40004] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves002:40004] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves002:40004] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves002:40004] [ 7] Ray(main+0xc5) [0x46d155]
[Braves002:40004] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3dc101ec9d]
[Braves002:40004] [ 9] Ray() [0x4691b9]
[Braves002:40004] *** End of error message ***
[Braves002:40005] [ 0] /lib64/libpthread.so.0() [0x3dc140f520]
[Braves002:40005] [ 1] Ray(_ZN15SearchDirectory8setCountEii+0xa) [0x50930a]
[Braves002:40005] [ 2]
Ray(_ZN8Searcher41call_RAY_SLAVE_MODE_COUNT_SEARCH_ELEMENTSEv+0x501) [0x500481]
[Braves002:40005] [ 3] Ray(_ZN11ComputeCore11processDataEv+0x66) [0x56f636]
[Braves002:40005] [ 4] Ray(_ZN11ComputeCore3runEv+0xd8) [0x576268]
[Braves002:40005] [ 5] Ray(_ZN7Machine5startEv+0x14b1) [0x46fdd1]
[Braves002:40005] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x190) [0x46d4d0]
[Braves002:40005] [ 7] Ray(main+0xc5) [0x46d155]
[Braves002:40005] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3dc101ec9d]
[Braves002:40005] [ 9] Ray() [0x4691b9]
[Braves002:40005] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 6 with PID 40005 on node 192.168.0.52 exited
on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
2 total processes killed (some possibly by mpiexec during cleanup)
------------------------------------------------------------------------------
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